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e726b1730d
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
34 lines
1.5 KiB
Text
34 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf'
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include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/gatk4/markduplicates/main.nf'
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workflow test_gatk4_markduplicates {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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GATK4_MARKDUPLICATES ( input, [], [] )
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}
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workflow test_gatk4_markduplicates_multiple_bams {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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] ]
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GATK4_MARKDUPLICATES ( input, [], [] )
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}
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workflow test_gatk4_markduplicates_multiple_cram_output {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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GATK4_MARKDUPLICATES_CRAM ( input, fasta, fai )
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}
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